The FASTQ files (n = 144) contain the demultiplexed raw sequence data (forward and reverse reads) from the 16S rRNA sequencing of the gut microbiota of C57BL/6J mice. Metadata.xlsx contains the sample and diet group information.

Data_bacteria_betaines.xlsx contains 6 tabs: 1) the gut microbial composition (as genus-level relative abundance) of C57BL/6J mice fed with diets enriched with rye bran and wheat aleurone; 2) betaine levels (as signal counts) in the colon contents of C57BL/6J mice fed with diets enriched with rye bran and wheat aleurone; 3) betaine levels in the caecal tissue of C57BL/6J mice fed with diets enriched with rye bran and wheat aleurone; 4) betaine levels in tissues of murine pathogen free (MPF) and germ-free (GF) C57BL/6NTac mice on a basal diet; 5) betaine levels in the in vitro model of the human gut; and 6) betaine levels in cereal samples. All betaine levels were analyzed with UPLC–QTOF-MS.